TE_MA_Paradoxus Analyses
R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.
When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
##
## ***** *** vcfR *** *****
## This is vcfR 1.10.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****## Loading required package: ade4## Registered S3 method overwritten by 'spdep':
## method from
## plot.mst ape##
## /// adegenet 2.1.2 is loaded ////////////
##
## > overview: '?adegenet'
## > tutorials/doc/questions: 'adegenetWeb()'
## > bug reports/feature requests: adegenetIssues()## Registered S3 methods overwritten by 'adegraphics':
## method from
## biplot.dudi ade4
## kplot.foucart ade4
## kplot.mcoa ade4
## kplot.mfa ade4
## kplot.pta ade4
## kplot.sepan ade4
## kplot.statis ade4
## scatter.coa ade4
## scatter.dudi ade4
## scatter.nipals ade4
## scatter.pco ade4
## score.acm ade4
## score.mix ade4
## score.pca ade4
## screeplot.dudi ade4##
## Attaching package: 'adegraphics'## The following objects are masked from 'package:ade4':
##
## kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
## s.label, s.logo, s.match, s.traject, s.value, table.value,
## triangle.class## Loading required package: ape##
## Attaching package: 'ape'## The following object is masked from 'package:adegraphics':
##
## zoom## Registered S3 method overwritten by 'pegas':
## method from
## print.amova ade4##
## Attaching package: 'pegas'## The following object is masked from 'package:ape':
##
## mst## The following object is masked from 'package:ade4':
##
## amova## The following object is masked from 'package:vcfR':
##
## getINFO## Warning: package 'lattice' was built under R version 3.6.2##
## Attaching package: 'gplots'## The following object is masked from 'package:stats':
##
## lowess## Loading required package: ggplot2## Google's Terms of Service: https://cloud.google.com/maps-platform/terms/.## Please cite ggmap if you use it! See citation("ggmap") for details.## Warning: package 'reshape2' was built under R version 3.6.2## Warning: package 'karyoploteR' was built under R version 3.6.1## Loading required package: regioneR## Warning: package 'regioneR' was built under R version 3.6.1## Loading required package: GenomicRanges## Warning: package 'GenomicRanges' was built under R version 3.6.1## Loading required package: stats4## Loading required package: BiocGenerics## Loading required package: parallel##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB## The following object is masked from 'package:adegraphics':
##
## score## The following object is masked from 'package:ade4':
##
## score## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, basename, cbind, colnames,
## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
## union, unique, unsplit, which, which.max, which.min## Loading required package: S4Vectors## Warning: package 'S4Vectors' was built under R version 3.6.1##
## Attaching package: 'S4Vectors'## The following object is masked from 'package:gplots':
##
## space## The following object is masked from 'package:base':
##
## expand.grid## Loading required package: IRanges## Warning: package 'IRanges' was built under R version 3.6.1## Loading required package: GenomeInfoDbVCF Analysis using vcfR
Fisher Test for Mutation Rate
Bedgraph Plots for Coverage - Old Style
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#
# BiocManager::install("karyoploteR")
# browseVignettes("karyoploteR")
#Function from Sam
# make_karyo_Spar337 <- function(mergefile,title) {
Chr_sizes_GR <- toGRanges("~/Dropbox/McQueary/Paradoxus_MA/Ref_Genome/337_chrm_sizes_red.bed") ## This is just a three column bed file of the chromosome sizes
gene_bed_GR <- toGRanges("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/Ref_Genome/337_sites_2.bed") ## This is just a three column bed file of the gene positions (just the gene entries from the gff3 file)
# supergene_GR <- GRanges(seqnames = "lg16",ranges=IRanges(7311525,18123987)) ## I made this GRanges object to delineate the supergene to add a block for it later
chroms <- c("Spar_I_RaGOO", "Spar_II_RaGOO", "Spar_III_RaGOO", "Spar_IV_RaGOO", "Spar_V_RaGOO", "Spar_VI_RaGOO", "Spar_VII_RaGOO", "Spar_VIII_RaGOO", "Spar_IX_RaGOO", "Spar_X_RaGOO", "Spar_XI_RaGOO", "Spar_XII_RaGOO", "Spar_XIII_RaGOO", "Spar_XIV_RaGOO", "Spar_XV_RaGOO","Spar_XVI_RaGOO")
# kp <- plotKaryotype(genome=Chr_sizes_GR)
# plot.params <- getDefaultPlotParams(plot.type = 1) ## This defines how the plot will generally be structured. See the options in the karyoploter documentation
# plot.params$data1height=8
# plot.params$data1outmargin = 4
# plot.params$data1inmargin = 2
# plot.params$ideogramheight = 2
# D20_A_cov <- read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/D20/D20-A_.bedgraph")
# str(D20_A_cov)
# colnames(D20_A_cov) <- c("chr","start","end","coverage")
# D20_A_GR <- makeGRangesFromDataFrame(D20_A_cov,seqnames.field = "chr", start.field = "start", end.field = "end", keep.extra.columns = TRUE)
# # ordered <- D20_A_GR[order(D20_A_GR$coverage, na.last = TRUE),] ## Sorts my DEG data to plot the top ten most DE genes later
# fc.ymax=ceiling(max(abs(D20_A_GR$coverage))) ## Define the maximum axes of the DEG plots
# fc.ymin=0 ## Define the minimum axes of the DEG plots
# TEs <- read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/TELocate/D20/raw/D20-A-R_R1_val_telocate_raw.TY1.bed")
# colnames(TEs) <- c("chr","start","end","TE")
# str(TEs)
# TEs.2 <- toGRanges(TEs)
# TEs.3 <- toDataframe(TEs.2)
# kpPlotRegions(kp1,data=TEs.2,col="#AACCFF",later.margin=0.01,border=NA,r0=0,r1=0.5)
## Place the DE dots in the region of the plot that I want
# kpAxis(kp, ymax=fc.ymax, ymin=fc.ymin,side = 2,cex=0.5,r0 = 0.15, r1 = 0.7) ## Add the axis for the DE dots
# kpAddMainTitle(kp,main=title) ## Add a title to the plot
# kpPlotRegions(kp,data = supergene_GR,col="red", r0=0,r1=0.1) ## add a box to show where the supergene is
# kpPlotMarkers(kp, ordered[1:10], labels = ordered[1:10]$Row.names, text.orientation = "vertical",adjust.label.position = TRUE,r0 = 0.75) ## Add markers for the top 10 most DE genes
#
## Load in, filter and format the DE data to be plotted. End result should be a GRanges object with extra columns of differential expression stats (logFC, FDR, etc)
# temp <- mergefile
# temp$chr <- as.character(temp$chr)
# temp.sig<-temp[(temp$FDR<=0.01 & grepl("lg",temp$chr)),]
# temp.sig <- temp.sig[complete.cases(temp.sig), ]
# DEG_GR <- makeGRangesFromDataFrame(temp.sig, seqnames.field = "chr",start.field = "start",end.field = "end",keep.extra.columns = TRUE)
#
## Begin generating the plot itself. If you want to change anything in the plot after first generating it, start again here.
# kp <- plotKaryotype(genome = Chr_sizes_GR, cytobands = gene_bed_GR,chromosomes = c("Spar_XVI_RaGOO"),plot.params = plot.params)
# ordered <- DEG_GR[order(DEG_GR$FDR, na.last = TRUE),] ## Sorts my DEG data to plot the top ten most DE genes later
# fc.ymax=ceiling(max(abs(DEG_GR$logFC))) ## Define the maximum axes of the DEG plots
# fc.ymin=0 ## Define the minimum axes of the DEG plots
# cex.val <- -log10(DEG_GR$FDR)/7 ## Sets the size for each gene dot based on significance
# col.over <- "#FFBD07AA" #Yellow
# col.under <- "#00A6EDAA" #Blue
# col.insig <- "#7F7F7F"
# sign.col <- rep(col.insig, length(DEG_GR)) ## This and the next two lines generate a an array of color entries linked to the genes to color the dots
# sign.col[(DEG_GR$logFC<0)&(DEG_GR$FDR<=0.01)] <- col.under
# sign.col[(DEG_GR$logFC>0)&(DEG_GR$FDR<=0.01)] <- col.over
# kpPoints(kp, data=DEG_GR, y=abs(DEG_GR$logFC), ymax=fc.ymax, ymin=fc.ymin,cex=cex.val, col=sign.col,r0 = 0.15, r1 = 0.7) ## Place the DE dots in the region of the plot that I want
# kpAxis(kp, ymax=fc.ymax, ymin=fc.ymin,side = 2,cex=0.5,r0 = 0.15, r1 = 0.7) ## Add the axis for the DE dots
# kpAddMainTitle(kp,main=title) ## Add a title to the plot
# kpPlotRegions(kp,data = supergene_GR,col="red", r0=0,r1=0.1) ## add a box to show where the supergene is
# kpPlotMarkers(kp, ordered[1:10], labels = ordered[1:10]$Row.names, text.orientation = "vertical",adjust.label.position = TRUE,r0 = 0.75) ## Add markers for the top 10 most DE genes
# } ## Make karyoplot for linearized genome (!!)
# ##################################################################################################
# ##################################################################################################
# # library(Sushi)
#
# # data(list=c("Sushi_DNaseI.bedgraph","Sushi_ChIPSeq_CTCF.bedgraph",
# # "Sushi_ChIPExo_CTCF.bedgraph"), package="Sushi")
#
# D20 = read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/D20/D20-A_.bedgraph")
# D20_TE = read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/TELocate/D20/raw/D20-A-R_R1_val_telocate_raw.TY1.bed")
#
# dd <- list(D20=D20_A_cov)#, D20_TE=D20_TE)
#
# png("bedgraphPlot.png", width = 1500, height = 1000)
# kp <- plotKaryotype(zoom="chr1:1-240865",main = "BedGraphs", cex=1)
# kpAddBaseNumbers(kp, tick.dist = 10e4, add.units = TRUE, cex=0.5)
# for(i in seq_len(length(dd))) {
# names(dd[[i]]) <- c("chr", "start", "end", "value")
# gr <- toGRanges(dd[[i]])
# # at <- autotrack(i, length(dd), margin = 0.1)
# kpPoints(kp, data=gr, ymax=max(gr$value), col=rainbow(10)[i])
# kpAddLabels(kp, labels = names(dd)[i], cex=0.5)
# }
# dev.off()
#
# str(D20)
#
# names(D20) <- c("chr", "start", "end", "value")
# gr <- toGRanges(D20)
# # at <- autotrack(D20, length(D20), margin = 0.1)
# kp <- plotKaryotype(main = "BedGraphs", cex=3)
# kpAddBaseNumbers(kp, tick.dist = 10e4, add.units = TRUE, cex=1.8)
# kpPoints(kp, data=gr, ymax=max(gr$value),col=rainbow(10)D20)
# kpAddLabels(kp, labels = names(D20), r0=at$r0, r1=at$r1)
############## This script works for me ###############
###################################################
### Call karyotype plot
## Specify which chromosome in this
# load in chromosome sizes and cytobands files
# {kp1 <- plotKaryotype(plot.type=2, genome=Chr_sizes_GR,cytobands=gene_bed_GR,chromosomes = c("Spar_XII_RaGOO"))
# # this tells the program to add base numbers (self-explanatory)
# kpAddBaseNumbers(kp1)
# # this plots whatever markers you tell it to - in this case, markers of TEs in this genome
# kpPlotMarkers(kp1, chr=TEs$chr, x=TEs$start, labels=TEs$TE,data.panel=2)
# # this plots the coverage in 10kb chunks bc that's what we computed
# kpBars(kp1, data=D20_A_GR, y1=D20_A_GR$coverage, ymax=max(D20_A_GR$coverage)/2, data.panel=1,col="blue")}
# # gives a plot of chromosome XII with coverage on top and TE locations on the bottom
## check out D20-1, look at chr VI first, then chr XVI
# D20_1_cov <- read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/D20/HM-D20-1.bedgraph")
# str(D20_1_cov)
# colnames(D20_1_cov) <- c("chr","start","end","coverage")
# D20_1_GR <- makeGRangesFromDataFrame(D20_1_cov,seqnames.field = "chr", start.field = "start", end.field = "end", keep.extra.columns = TRUE)
# TEs_1 <- read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/TELocate/D20/raw/HM-D20-1_R1_001_val_telocate.bed")
# colnames(TEs_1) <- c("chr","start","end","TE")
# str(TEs_1)
# TEs_1 <- toGRanges(TEs_1)
# TEs.3 <- toDataframe(TEs.2)
# {kp1 <- plotKaryotype(plot.type=2, genome=Chr_sizes_GR,cytobands=gene_bed_GR,chromosomes = c("Spar_XII_RaGOO"))
# # this tells the program to add base numbers (self-explanatory)
# kpAddBaseNumbers(kp1)
# # this plots whatever markers you tell it to - in this case, markers of TEs in this genome
# kpPlotMarkers(kp1, data=TEs_1, chr=TEs_1$chr, x=TEs_1$start, labels=TEs_1$TE, data.panel=2)
# # this plots the coverage in 10kb chunks bc that's what we computed
# kpBars(kp1, data=D20_1_GR, y1=D20_1_GR$coverage, ymax=max(D20_1_GR$coverage)/2, data.panel=1,col="green", r0=0, r1=0.25)
# }
# # gives a plot of chromosome XII with coverage on top and TE locations on the bottom
# kpBars(kp1, data=D20_A_GR, y1=D20_A_GR$coverage, ymax=max(D20_A_GR$coverage)/2, data.panel = 1, col="blue",r0=0.25, r1=0.5)
# kpPlotCoverage(kp1, data=D20_A_GR, data.panel = 1, col="blue",r0=0.25, r1=0.5)
# You need to make sure that the chromosome you call in plotKaryotype is present in the TE file and that the chromosome names match (i.e. the TE files don't have _RaGOO at the end of their chromosome names)
####################################################################################################################
#### Trying with .depth file generated by Audrey (this file has depth at every site in the genome )
# D20_10_depth <- read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/D20/HM-D20-10.depth")
# str(D20_10_depth)
# colnames(D20_10_depth) <- c("chr","pos","coverage")
# D20_10_GR <- makeGRangesFromDataFrame(D20_10_depth,seqnames.field = "chr", start.field = "pos", end.field = "pos", keep.extra.columns = TRUE)
#
# TEs_10 <- read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/TELocate/D20/raw/HM-D20-10_R1_001_val_telocate_raw.TY1.bed")
# colnames(TEs_10) <- c("chr","start","end","TE")
# str(TEs_10)
# TEs_10 <- toGRanges(TEs_10)
# TEs.3 <- toDataframe(TEs.2)
# mid.regs <- createRandomRegions(nregions = 6000, length.mean = 5000000, length.sd = 1000000, non.overlapping = FALSE)
plotDepthTELocations <- function(depthFile,teFile,sample,chroms) {
# load in depth table
depth <- read.table(depthFile)
#add column names
colnames(depth) <- c("chr","pos","coverage")
# turn file into a GRanges object
depthGR <- makeGRangesFromDataFrame(depth,seqnames.field = "chr", start.field = "pos", end.field = "pos", keep.extra.columns = TRUE)
# load in TE file (from TELocate)
TEs <- teFile
# add column names
colnames(TEs) <- c("chr","start","end","TE")
# make GRanges object from TE file
TEs <- toGRanges(TEs)
# make pdf plot for all chromosomes: depth + TE locations
# {pdf(paste("depthTELocate",sample,chroms,".pdf",sep=""))
#general plotKaryotype command (same for all samples)
kp <- plotKaryotype(genome=Chr_sizes_GR, cytobands=gene_bed_GR, chromosomes= chroms, cex=0.5, main = paste(sample,chroms,sep="_"))
# this tells the program to add base numbers (self-explanatory)
# can specify how spaced out you want them using tick.dist
# units adds "kb", "mb", etc
kpAddBaseNumbers(kp,tick.dist = 100000,add.units = TRUE)
# this plots whatever markers you tell it to - in this case, markers of TEs in this genome
# can specify colors of lines and text, distance labels are from each other, etc
# data panel = 2 specifies that it is the bottom panel
kpPlotMarkers(kp, data=TEs, chr=TEs$chr, x=TEs$start, labels=TEs$TE, data.panel=2,cex=0.5, text.orientation = "horizontal", line.color = "pink", label.color = "purple", label.dist = 0.01, max.iter = 1000)
# this plots coverage at every base along each chromosome from depth file
# data panel = 1 specifies it is the top panel
kpBars(kp, data=depthGR, y1=depthGR$coverage, ymax=max(depthGR$coverage)/2, data.panel=1)
# dev.off() }
}
depthFileNamesD20 <- list.files(path = "/Users/hollymcqueary/Dropbox/depthFiles/D20", pattern="*.depth",full.names = TRUE)
testDepth <- read.table("/Users/hollymcqueary/Dropbox/depthFiles/D20/HM-D20-24.depth")
consensusTEs <- read.table("/Users/hollymcqueary/Dropbox/McQueary/Paradoxus_MA/BedGraphs/TELocate/consensusTEs.txt")
# plotDepthTELocations(testDepth,consensusTEs,"Sample24All","Spar_II_RaGOO")
# plotDepthTELocations(testDepth,consensusTEs,"Sample24All",chroms)
# i=1
sampleNames <- c("Sample1","Sample10","Sample11","Sample12","Sample13","Sample14","Sample15","Sample16","Sample17","Sample18","Sample19","Sample2","Sample20","Sample21","Sample22","Sample23","Sample24","Sample25","Sample26","Sample27","Sample28","Sample29","Sample3","Sample30","Sample31","Sample32","Sample33","Sample34","Sample35","Sample36","Sample37","Sample38","Sample39","Sample4","Sample40","Sample41","Sample42","Sample43","Sample44","Sample45","Sample46","Sample47","Sample48","Sample5","Sample6","Sample8","Sample9","Ancestor")
sampleNames[12]## [1] "Sample2"length(sampleNames)## [1] 48length(depthFileNamesD20)## [1] 48plotDepthTELocations(depthFileNamesD20[17],consensusTEs,sampleNames[17],"Spar_II_RaGOO")## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands.
## Using 'gpos50' (gray) for all of them
plotDepthTELocations(depthFileNamesD20[3],consensusTEs,sampleNames[3],"Spar_X_RaGOO")## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands.
## Using 'gpos50' (gray) for all of them
plotDepthTELocations(depthFileNamesD20[17],consensusTEs,sampleNames[17],"Spar_IX_RaGOO")## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands.
## Using 'gpos50' (gray) for all of them
plotDepthTELocations(depthFileNamesD20[3],consensusTEs,sampleNames[3],"Spar_XIV_RaGOO")## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands.
## Using 'gpos50' (gray) for all of them
plotDepthTELocations(depthFileNamesD20[12],consensusTEs,sampleNames[12],"Spar_XIV_RaGOO")## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands.
## Using 'gpos50' (gray) for all of them
plotDepthTELocations(depthFileNamesD20[13],consensusTEs,sampleNames[13],"Spar_XV_RaGOO")## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands.
## Using 'gpos50' (gray) for all of them
for(i in 1:48) {
plotDepthTELocations(depthFileNamesD20[i],consensusTEs,sampleNames[i],"Spar_VI_RaGOO")
}## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands.
## Using 'gpos50' (gray) for all of them## Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
## Warning in ideogram.plotter(kp, ...): No 'gieStain' column found in cytobands. Using 'gpos50' (gray) for all of them
## Warning in ideogram.plotter(kp, ...): The 2 combined objects have no sequence levels in common. (Use
## suppressWarnings() to suppress this warning.)
#, r0=0, r1=0.25)}
# kpBars(kp1, data=D20_A_GR, y1=D20_A_GR$coverage, ymax=max(D20_A_GR$coverage)/2, data.panel = 1, col="blue",r0=0.25, r1=0.5)
# kpPlotCoverage(kp1, data=D20_10_GR, data.panel = 1, col="blue",r0=0.25, r1=0.5)}
# gives a plot of chromosome XII with coverage on top and TE locations on the bottom
# You need to make sure that the chromosome you call in plotKaryotype is present in the TE file and that the chromosome names match (i.e. the TE files don't have _RaGOO at the end of their chromosome names)
# kpPlotRegions(kp10, data=gene_bed_GR,data.panel = 2)
##### Use kpRect to plot TEs so you can use start and stop positions to show length of TE
# kpPlotRegions(kp10, data=TEs_10, border=NA, r0=0.2, r1=1, data.panel = 2)Packages used in this analysis
library(vcfR)
library(adegenet)
library(adegraphics)
library(pegas)
library(StAMPP)
library(lattice)
library(gplots)
library(ape)
library(ggmap)
library(pinfsc50)
library(reshape2)
library(ggplot2)
library(karyoploteR)
library(GenomicRanges)